Utah Valley University - BIOL490R (Special Topics)
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Make sure you’ve watched the videos above and can navigate in your command line terminal.
Do you know what the following commands do?
pwd
cd ~
cd ..
ls -a
ls -lFor your consideration:
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How many sequences are stored (in total) in the fastq files associated with Assignment_4?
How many sequences end with the seqeunce “AT” in each fastq file?
Which fastq file associated with Assignment_4 contains the following sequence:
CCTTCATGCTGTCCTGCAATTACGATAGCATTTCTTTGACGACGACFor your consideration:
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Here’s an awful-looking one-line command that prints out the phylum from each line of Chapter_7_Practice_File_2.txt along with a number sequence next to it showing which line of the file it came from.
It uses both process and command substitution, but essentially, it’s just the paste command pasting together the phylum in the first field and the numbers 1-34 in the second field
I want you to break it apart, looking at each component and understand why it works!
paste <(cat Chapter_7_Practice_File_2.txt | cut -d ";" -f 2) <(seq $(wc -l Chapter_7_Practice_File_2.txt | cut -d " " -f 1))If you wanted to use process substitution again to extend this whole command in order to add a header to the output, what would you do? (i.e., add a first row that is “PHYLUM LINE_NUMBER”)
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Work through BDS Chapter 6
Case Study 2 - Reproducibly downloading stuff (BDS p. 120)
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Video series on the CHPC
SLURM commands cheat sheet
SLURM Presentation from CHPC
How public key encryption actually works
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sra-toolkit is available as a module on the CHPC, but you’ll need to configure it before use using
vdb-config -iprefetch instructions
fastq-dump instructions from the Edwards Lab
FileZilla is a free FTP client that really comes in handy for moving files to and from remote servers
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Work through BDS Chapter 12
Remember that “create a new project” script you wrote at the beginning of the semester?
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Build a bash script that can:
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The duct tape of bioinformatics
Good pipelines need:
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Case Study 3 - Assemble a metagenome on the remote cluster
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Case Study 4 - Download NCBI marker genes and use Unix tools to build a custom RDP-Classifier-compatible reference database
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